[Freesurfer] make_average_subject command error

External Email - Use Caution Dear Freesurfer experts, We're trying to make an average subject for group analysis using Freesurfer 7.1, but the make_average_subject command exits with errors after calling make_average_surf: MakeAverageSurf(): 129 lh pial sphere.reg talairach.x

Re: [Freesurfer] Command terminated by signal 11 when execute mris_place_surface

External Email - Use Caution Hello freesurfer experts , I change the command and reduce the threads from 200 to 50 , seems ok now , I use the cluster to run the jobs and submit jobs to cluster, I found there have several jobs assigned to the same node , do this be ok to run differe

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

External Email - Use Caution Dear Yujing, Thank you for your kind help (and sorry for my late reply). It worked with the added flag; - measures thickness. I appreciate your advice on adding directives at the end of the recon-all command. Best, Asuka _

[Freesurfer] Calculation of MRI intensity

External Email - Use Caution Hi Freesurfer Team, Please I want to calculate the mean intensity of a skullstripped MRI image. I do not want to use recon-all because I do not want to parcellate or segment it. Is there such utility or function in freesurfer? Thank you. Sincerely, E

Re: [Freesurfer] make_average_subject command error

If you run recon-all, ?h.pial will appear as symbolic links to ?h.pial.T1. Here is the list of symbolic links you should find in your subject/surf directory: rh.pial -> rh.pial.T1 lh.pial -> lh.pial.T1 rh.fsaverage.sphere.reg -> rh.sphere.reg lh.fsaverage.sphere.reg -> lh.sphere.reg rh.white.K

Re: [Freesurfer] FW: Create a Binarized ROI for Surface

Sorry, I don't understand what you are asking. Can you elaborate? On 1/19/2024 4:37 PM, Na, Xiaoxu wrote: External Email - Use Caution Hi Dr. Doug, Thanks for your prompt reply! I’m sorry it was not clear. Basically, I would like to extract the cortical volume for each subject using

Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

Can you run it with -debug as the first option, capture the output, and send it to me? It will be a lot of output, so just capture it in a file and send the file, eg preproc-sess -debug -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -force | tee pps.log

Re: [Freesurfer] MRIread and RAS orientation

The vol structure will reflect how the volume is stored on disk. If you have two files that have the same structure (ie, order of rows, cols, slices) then they will have the same vol in matlab regardless of the header orientation. On 1/23/2024 11:00 AM, Fotiadis, Panagiotis wrote: Ex

Re: [Freesurfer] Calculation of MRI intensity

I think mri_segstats –i option will do that - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Wednesday, February 7, 2024 8:12 AM To: Freesurfer support list Subject: [Freesurfer] Calculation of

Re: [Freesurfer] Recon-all Longitudinal Talairach issue

Can you send the recon-all.log file that contains the error? On 1/24/2024 4:01 AM, Kapteijns, Kirsten wrote: External Email - Use Caution Dear all, I have run recon-all successfully on multiple subjects on multiple timepoints. If I open the mri folder, it shows the correct talairach

Re: [Freesurfer] Freesurfer Intensity representation

See this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0 on multimodal integration. Basically, you will need to run mri_vol2vol to map your MPF volume to the anatomical/conformed space, then run mri_segstats passing it the segmentation you want to use and the converte

Re: [Freesurfer] T1 maps longitudinal data

Currently, you'd have to convert them  to  t1-weighted images and then run recon-all on that. I think there is software out there to do this if you go the t1 maps from an mp2rage scan On 1/25/2024 11:57 AM, AJ wrote: External Email - Use Caution Hi, I have T1 relaxation maps over 4 t

Re: [Freesurfer] No ROI name in summary of MNI305 group analysis

Try adding -seg fsaverage aparc+aseg.mgz On 1/26/2024 4:59 AM, wangzhiwei3233 wrote: External Email - Use Caution Dear Gouglas, Thank you for your replay. There is still no ROI name in the summary after adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat. My updated command is

Re: [Freesurfer] Calculation of MRI intensity

you will have to binarize it first, eg, mri_binarize --i inputimage.mgz --min threshold --o binary.mgz, then run mri_segstats --seg binary.mgz --id 1 --i inputimage.mgz --sum sum.dat On 2/7/2024 8:55 AM, Huang, Yujing wrote: I think mri_segstats –i option will do that - https://surfer.nmr.mg

[Freesurfer] [TRACULA] how to setup with opposite phase-encoding

External Email - Use Caution Hi, I've been trying to use TRACULA on my data, trying to setup a configuration file but I am having some difficulty on how to incorporate my data. I have a DWI scan with 65 volumes (1 b0 image, 64 with b = 1000) I also have separate volumes for b0 p

[Freesurfer] Synthsr command !

External Email - Use Caution Dear Juan and FreeSurfer developers, I am trying to run the *mri_synthsr *command on a MacPro M2 Max chip (OS 13.6.4) - but somehow, I am getting the following error when I try to run this command. I am using FreeSurfer's 7.4.1 version. *Illegal instr